3D slicing using Dynamic Paint leaves holes where there shouldnt be any
You could simplified file to make it smaller ... just a Plane and one problematic stone, like that you could notice it works. So why it is not working in group? I would say for its overlapping geometry.
I can imagine that hole in place of crossing stones , but it happens just it is crossed somewhere. If you move stone behind it is fine.
You can try Remesh Modifier &gt; Voxel &gt; 0.001 m, before DP, but it would be very intensive calculation, but it worked ...

Or Separate stones by Loose parts set them Rigid Body (create a collision box) and let simulate for a few frames just to solve overlapping. Than merge them back into one object for DP.